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GPU accelerated implementation of density functional theory for hybrid QM/MM simulations
(American Chemical Society, 2014-02)
The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density ...
QM-MM investigation of the reaction products between nitroxyl and O2 in aqueous solution
(Elsevier Science, 2008-09)
By means of combined quantum-classical molecular (QM/MM) dynamics simulations, we investigated the structural properties and the vibrational spectra in aqueous solution of four possible intermediate species of the oxidation ...
QM-MM Investigation of the Reaction of Peroxynitrite with Carbon Dioxide in Water
(American Chemical Society, 2007)
Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code
(Frontiers Media SA, 2018-03)
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with ...
How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study
(American Chemical Society, 2009-05)
Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, ...
Study of the role of Mg2+ in dsRNA processing mechanism by bacterial RNase III through QM/MM simulations
(Springer, 2019-11)
The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. ...
QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential Cytochrome p450 of Mycobacterium tuberculosis
(Wiley, 2013-12)
Among 20 p450s of Mycobacterium tuberculosis (Mt), CYP121 has received an outstanding interest, not only due to its essentiality for bacterial viability but also because it catalyzes an unusual carbon-carbon coupling ...
Spectral signatures of canthaxanthin translocation in the orange carotenoid protein
(American Chemical Society, 2020-12)
The orange carotenoid protein (OCP) is involved in the photoprotective processes in cyanobacteria via nonphotochemical quenching. Triggered by blue-green light absorption, the carotenoid chromophore undergoes translocation, ...
Spectral signatures of canthaxanthin translocation in the orange carotenoid protein
(American Chemical Society, 2020-12)
The orange carotenoid protein (OCP) is involved in the photoprotective processes in cyanobacteria via nonphotochemical quenching. Triggered by blue-green light absorption, the carotenoid chromophore undergoes translocation, ...
Spectroscopy in Complex Environments from QM-MM Simulations
(American Chemical Society, 2018-04)
The applications of multiscale quantum-classical (QM-MM) approaches have shown an extraordinary expansion and diversification in the last couple of decades. A great proportion of these efforts have been devoted to interpreting ...